Literature DB >> 27186992

Water Determines the Structure and Dynamics of Proteins.

Marie-Claire Bellissent-Funel1, Ali Hassanali2, Martina Havenith3, Richard Henchman4, Peter Pohl5, Fabio Sterpone6, David van der Spoel7, Yao Xu3, Angel E Garcia8.   

Abstract

Water is an essential participant in the stability, structure, dynamics, and function of proteins and other biomolecules. Thermodynamically, changes in the aqueous environment affect the stability of biomolecules. Structurally, water participates chemically in the catalytic function of proteins and nucleic acids and physically in the collapse of the protein chain during folding through hydrophobic collapse and mediates binding through the hydrogen bond in complex formation. Water is a partner that slaves the dynamics of proteins, and water interaction with proteins affect their dynamics. Here we provide a review of the experimental and computational advances over the past decade in understanding the role of water in the dynamics, structure, and function of proteins. We focus on the combination of X-ray and neutron crystallography, NMR, terahertz spectroscopy, mass spectroscopy, thermodynamics, and computer simulations to reveal how water assist proteins in their function. The recent advances in computer simulations and the enhanced sensitivity of experimental tools promise major advances in the understanding of protein dynamics, and water surely will be a protagonist.

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Year:  2016        PMID: 27186992     DOI: 10.1021/acs.chemrev.5b00664

Source DB:  PubMed          Journal:  Chem Rev        ISSN: 0009-2665            Impact factor:   60.622


  107 in total

1.  A Biophysical Perspective on Enzyme Catalysis.

Authors:  Pratul K Agarwal
Journal:  Biochemistry       Date:  2018-12-18       Impact factor: 3.162

2.  Mirror-image antiparallel β-sheets organize water molecules into superstructures of opposite chirality.

Authors:  Ethan A Perets; Daniel Konstantinovsky; Li Fu; Jiantao Chen; Hong-Fei Wang; Sharon Hammes-Schiffer; Elsa C Y Yan
Journal:  Proc Natl Acad Sci U S A       Date:  2020-12-14       Impact factor: 11.205

3.  Allosteric control of antibody-prion recognition through oxidation of a disulfide bond between the CH and CL chains.

Authors:  Jun Zhao; Ruth Nussinov; Buyong Ma
Journal:  Protein Eng Des Sel       Date:  2016-11-29       Impact factor: 1.650

Review 4.  Synthetic, Switchable Enzymes.

Authors:  Vic Norris; Sergey N Krylov; Pratul K Agarwal; Glenn J White
Journal:  J Mol Microbiol Biotechnol       Date:  2017-04-28

5.  Binding Thermodynamics and Kinetics Calculations Using Chemical Host and Guest: A Comprehensive Picture of Molecular Recognition.

Authors:  Zhiye Tang; Chia-En A Chang
Journal:  J Chem Theory Comput       Date:  2017-12-14       Impact factor: 6.006

6.  Direct Observation of Nanosecond Water Exchange Dynamics at a Protein Metal Site.

Authors:  Monika Stachura; Saumen Chakraborty; Alexander Gottberg; Leela Ruckthong; Vincent L Pecoraro; Lars Hemmingsen
Journal:  J Am Chem Soc       Date:  2016-12-20       Impact factor: 15.419

7.  Fast pressure-jump all-atom simulations and experiments reveal site-specific protein dehydration-folding dynamics.

Authors:  Maxim B Prigozhin; Yi Zhang; Klaus Schulten; Martin Gruebele; Taras V Pogorelov
Journal:  Proc Natl Acad Sci U S A       Date:  2019-03-05       Impact factor: 11.205

8.  Water dynamics: Gliding and trudging.

Authors:  Yoshimitsu Itoh; Takuzo Aida
Journal:  Nat Chem       Date:  2017-09-22       Impact factor: 24.427

9.  Local and global anatomy of antibody-protein antigen recognition.

Authors:  Meryl Wang; David Zhu; Jianwei Zhu; Ruth Nussinov; Buyong Ma
Journal:  J Mol Recognit       Date:  2017-12-08       Impact factor: 2.137

10.  Biophysical Characterization of a Disabled Double Mutant of Soybean Lipoxygenase: The "Undoing" of Precise Substrate Positioning Relative to Metal Cofactor and an Identified Dynamical Network.

Authors:  Shenshen Hu; Adam R Offenbacher; Erin M Thompson; Christine L Gee; Jarett Wilcoxen; Cody A M Carr; Daniil M Prigozhin; Vanessa Yang; Tom Alber; R David Britt; James S Fraser; Judith P Klinman
Journal:  J Am Chem Soc       Date:  2019-01-15       Impact factor: 15.419

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